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IP Update: Affymetrix; GE; University of North Carolina; Siemens; Sanofi; and More

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Affymetrix of Santa Clara, Calif., has received US Patent No. 8,062,844, "Use of acid scavengers for the synthesis of standard length and long-mer nucleic acid arrays." According to the patent, protective groups, cleavable with activatable deprotecting reagents, are employed to achieve a highly sensitive, high resolution, combinatorial synthesis of pattern arrays of diverse polymers. In a preferred embodiment, the activatable deprotecting reagent is a photoacid generator and the protective groups are N,N-dimethyltryptamine for nucleic acids and N-tert-butoxycarbonyl for amino acids. The inventors claim that the method is useful for the solid phase combinatorial synthesis of polymers.


Affymetrix has also received US Patent No. 8,067,164, "Microarray system with improved sequence specificity." The patent describes an array-based method for nucleic acid sequence detection with improved specificity that allows for detection of genetic variation, from SNPs to more complex sequence variation patterns. The array consists of short, synthetic oligonucleotide probes attached to a solid surface, which are hybridized to single-stranded targets. The single-stranded targets can be produced using a method that employs primers modified on the 5' end to prohibit degradation by a 5'-exonuclease that is introduced to degrade the unprotected strand, according to the patent. Also provided are printing buffers for the immobilization of oligonucleotide probes to an array surface.


Affymetrix has also received US Patent No. 8,067,578, "Substrate preparation process." The patent claims a method for synthesizing arrays of oligonucleotide probes on a surface of a substrate, which includes: providing a reaction chamber consisting of a door connected by hinges to the reaction chamber; placing the substrate into the reaction chamber, where the reaction chamber also includes a number of automatic alignment pins that contact the substrate; closing the door of the reaction chamber; and exposing the surface of the substrate to a solution consisting of a monomer so that at least one monomer binds to the surface of the substrate.


GE of Niskayuna, NY, has received US Patent No. 8,063,385, "Method and apparatus for ultraviolet scan planning." The method involves transmitting light of a preselected wavelength onto a tissue sample, where the light induces the tissue sample to autofluoresce; identifying the center location of the tissue sample using the autofluoresced light; correlating the coordinates of the center location of the tissue sample on the solid support using an x, y-coordinate system; and mapping the coordinates of the tissue sample on the solid support to differentiate tissue sample containing regions from blank regions on the solid support.


The University of North Carolina of Charlotte has received US Patent No. 8,065,089, "Methods and systems for analysis of dynamic biological pathways." The patent claims a hierarchical computational method to predict the expression value of genes in time-series microarray data. The method includes the step of applying a nonlinear independent component analysis algorithm that extracts the major components covering all considered genes. An autoregressive exogenous model may subsequently be used to quantitatively express the dynamic interactions of all components with each other. Then, using the predicted values for the components, and the nonlinear independent component analysis in the inverse form, the data may be used to predict the expression parameters for individual genes. The method may be used to analyze eukaryotic gene expression throughout the cell cycle.


Siemens of Munich, Germany, has received US Patent No. 8,067,249, "Method for functionalizing biosensor chips." According to the patent, the biosensors are based on semiconductor chips mounted on a finished processed wafer. They are provided with sensor fields that are arranged in an array format for carrying out a functionalization with organic molecules such as nucleic acids like DNA, RNA, and PNA or with their derivatives, proteins, sugar molecules, or antibodies.


Hee Tae Jung, Sang Yup Lee, Dae Hwan Jung, and Young Koan Ko of Daejeon, Korea, and Byung Hun Kim of Seoul have received US Patent No. 8,067,341, "Method for fabricating a biochip using the high density carbon nanotube film or pattern." The described chips consist of a bio-receptor attached by means of an exposed chemical functional group on a surface of a high-density CNT film or pattern produced by repeated lamination of CNTs on a substrate with exposed amine groups. CNT biochips may be used to measure an electrical or electrochemical signal using both conductor and semiconductor properties of the CNT. Upon fluorescent measurement of DNA hybridization using a CNT-DNA chip it is possible to show more distinct signals useful for genotyping, mutation detection, pathogen identification and the like, according to the patent.


Sanofi of Paris has received US Patent No. 8,067,581, "Biomolecules having multiple attachment moieties for binding to a substrate surface." Compounds relating to attachment chemistries for binding biomolecules to a substrate surface are described. The compounds can be used to bind biomolecules that can include a single nucleic acid, oligonucleotides, polynucleotides, DNAs, RNAs, proteins, peptides, enzymes, antibodies, cyclohexyl nucleic acids, methyl or methoxy phosphate nucleic acids, peptide nucleic acids, and pyranosyl RNAs.


Ventana Medical Systems of Tucson, Ariz., now part of Roche, has received US Patent No. 8,068,988, "Method for automated processing of digital images of tissue micro-arrays (TMA)." The method permits the automatic digital imaging of a tissue microarray with multiple cores created from needle biopsies or other techniques. A subsequent analysis enables users to reach a medical conclusion such as a medical diagnosis or prognosis. The method provides reliable automatic core gridding and boundary detection including detection of overlapping or touching cores on a grid.


Integrated DNA Technologies of Skokie, Ill., has received US Patent No. 8,068,991, "Systems and methods for transmitting pathogen related information and responding." The methods include receiving data identifying pathogens present within samples obtained from an individual through use of microfluidic chips; receiving input associated with the individual, including physical characteristics, medical history information, and other information; and processing the input and the data by determining time values associated with the pathogens and values associated with agent usage by the one or more individuals; determining whether a relationship exists between the agent usage and pathogens; and determining agent dosages.

The Scan

For Better Odds

Bloomberg reports that a child has been born following polygenic risk score screening as an embryo.

Booster Decision Expected

The New York Times reports the US Food and Drug Administration is expected to authorize a booster dose of the Pfizer-BioNTech SARS-CoV-2 vaccine this week for individuals over 65 or at high risk.

Snipping HIV Out

The Philadelphia Inquirer reports Temple University researchers are to test a gene-editing approach for treating HIV.

PLOS Papers on Cancer Risk Scores, Typhoid Fever in Colombia, Streptococcus Protection

In PLOS this week: application of cancer polygenic risk scores across ancestries, genetic diversity of typhoid fever-causing Salmonella, and more.